Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK8

Cell type

Cell type Class
Blood
Cell type
SET-2
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
SET2
cell line
SET2
cell type
essential thrombocythemia
treatment protocol
untreated
chip epitope
CDK8
ca sensitivity
sensitive

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries for Illumina sequencing were prepared using the Illumina TruSeq ChIP Sample Preparation kit with the following exceptions. After end-repair and A-tailing, ChIP DNA or whole cell extract DNA was ligated to Illumina RNA adaptors with unique indices. Alternatively, libraries were prepared using the KAPA Hyper Prep Kit for Illumina and ligated to unique Bioo Scientific NEXTflex barcode adaptors. Following ligation, libraries were amplified with 16-18 cycles of PCR and were then size-selected using a 2% gel cassette in the Pippin Prep System from Sage Science. For histone modifications and RNA pol II, DNA fragments of size 200-500bp were captured. For CDK8 and MED1, DNA fragments of size 200-450bp were captured. Libraries were quantified by qPCR utilizing the KAPA Biosystems Illumina Library Quantification kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
28756954
Reads aligned (%)
91.6
Duplicates removed (%)
4.4
Number of peaks
6480 (qval < 1E-05)

hg38

Number of total reads
28756954
Reads aligned (%)
93.3
Duplicates removed (%)
3.3
Number of peaks
6709 (qval < 1E-05)

Base call quality data from DBCLS SRA